Variant report

Variant	rs678892
Chromosome Location	chr15:55632859-55632860
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55631303..55633200-chr15:55699872..55702073,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261652	Chromatin interaction
ENSG00000260916	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11635126	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595377	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12708446	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12902710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12902902	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12912490	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs2414406	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2439048	0.90[ASW][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs28459661	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28685005	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28799296	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28852495	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35715239	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4354865	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4558357	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs515341	0.90[ASW][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs569333	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs574923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493776	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7164608	0.94[AMR][1000 genomes]
rs7166125	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8025833	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8026689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8032594	0.94[CHB][hapmap];0.87[CHD][hapmap]
rs8036244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8036345	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8036729	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8037056	1.00[ASW][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8039771	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8040540	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8182068	0.94[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv904243	chr15:55627528-55734158	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs678892	PIGB	cis	lung	GTEx
rs678892	SLC27A2	cis	parietal	SCAN
rs678892	PIGB	cis	Esophagus Muscularis	GTEx
rs678892	PIGB	cis	Artery Tibial	GTEx
rs678892	RAB27A	cis	parietal	SCAN
rs678892	PIGB	cis	Nerve Tibial	GTEx
rs678892	ZNF214	trans	parietal	SCAN
rs678892	SCG3	cis	parietal	SCAN
rs678892	RFX7	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55640000	Weak transcription	Gastric	stomach
2	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
3	chr15:55612000-55635400	Weak transcription	Fetal Brain Female	brain
4	chr15:55612000-55636000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:55612000-55636000	Weak transcription	Brain Germinal Matrix	brain
6	chr15:55612000-55636400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:55612000-55665000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:55612000-55671000	Weak transcription	Right Ventricle	heart
9	chr15:55612000-55671000	Weak transcription	Small Intestine	intestine
10	chr15:55612400-55635600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:55612600-55640400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:55612600-55650200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:55612600-55663600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:55612600-55675600	Weak transcription	Aorta	Aorta
15	chr15:55612800-55635800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:55612800-55640400	Weak transcription	NHLF	lung
17	chr15:55612800-55649600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:55612800-55677600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:55614800-55649000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr15:55617000-55635400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:55617000-55635600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:55618800-55633800	Weak transcription	Stomach Mucosa	stomach
23	chr15:55619600-55633600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:55619600-55633800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:55619600-55640000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:55619800-55635400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:55619800-55636000	Weak transcription	HMEC	breast
28	chr15:55619800-55637600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr15:55620400-55658000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr15:55620800-55636800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:55621000-55635200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:55621600-55636800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr15:55621800-55635400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:55623000-55652600	Weak transcription	Psoas Muscle	Psoas
35	chr15:55623400-55642200	Weak transcription	Hela-S3	cervix
36	chr15:55623600-55635600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr15:55623600-55636000	Weak transcription	NHDF-Ad	bronchial
38	chr15:55623800-55635600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:55623800-55660200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:55624000-55635800	Weak transcription	NHEK	skin
41	chr15:55624000-55642800	Weak transcription	Esophagus	oesophagus
42	chr15:55624200-55640400	Weak transcription	Spleen	Spleen
43	chr15:55624800-55635400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:55625000-55636600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr15:55625200-55633600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr15:55625200-55634600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr15:55625200-55639000	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr15:55625200-55643000	Strong transcription	Primary T cells from cord blood	blood
49	chr15:55625800-55637000	Strong transcription	Primary B cells from cord blood	blood
50	chr15:55626000-55633600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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